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- EMDB-54440: Cellular environment of FIB-sectioned yeast cell overexpressing B... -

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Basic information

Entry
Database: EMDB / ID: EMD-54440
TitleCellular environment of FIB-sectioned yeast cell overexpressing Brr6(I149D)
Map dataTomogram of FIB-sectioned yeast cell overexpressing Brr6(AH*)
Sample
  • Organelle or cellular component: Cellular environment of FIB-sectioned Saccharomyces cerevisiae cell
KeywordsTomogram of FIB-milled yeast cell overexpressing Brr6(I149D) / TRANSPORT PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsFischer JS / Wojtynek M / Kumar A / Baird HJM / Radilova K / Maslennikova D / Ramachandran K / Becker AN / Agote Aran A / Loffreda A ...Fischer JS / Wojtynek M / Kumar A / Baird HJM / Radilova K / Maslennikova D / Ramachandran K / Becker AN / Agote Aran A / Loffreda A / Kralt A / Jagannathan M / Dey G / Kutay U / Vanni S / Weis K
Funding support Switzerland, European Union, 6 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMAG-3_20935 Switzerland
Swiss National Science Foundation310030_208213 Switzerland
Swiss National Science Foundation205603 Switzerland
Swiss National Science FoundationTMAG-3_209245 Switzerland
European Research Council (ERC)101078291European Union
European Research Council (ERC)KaryodynEVOEuropean Union
CitationJournal: To Be Published
Title: Cellular environment of FIB-sectioned yeast cell overexpressing Brr6(I149D)
Authors: Fischer JS / Wojtynek M / Kumar A / Baird HJM / Radilova K / Maslennikova D / Ramachandran K / Becker AN / Agote Aran A / Loffreda A / Kralt A / Jagannathan M / Dey G / Kutay U / Vanni S / Weis K
History
DepositionJul 17, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54440.png

Downloads & links

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Map

FileDownload / File: emd_54440.map.gz / Format: CCP4 / Size: 7.7 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationTomogram of FIB-sectioned yeast cell overexpressing Brr6(AH*)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.6 Å/pix.
x 700 pix.
= 4621.377 Å		6.6 Å/pix.
x 2880 pix.
= 19013.666 Å		6.6 Å/pix.
x 2046 pix.
= 13507.625 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.60197 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1241.0 - 1049.0
Average (Standard dev.)54.354213999999999 (±133.835919999999987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-417417-350
Dimensions28802046700
Spacing20462880700
CellA: 13507.625 Å / B: 19013.666 Å / C: 4621.377 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cellular environment of FIB-sectioned Saccharomyces cerevisiae cell

EntireName: Cellular environment of FIB-sectioned Saccharomyces cerevisiae cell
Components
  • Organelle or cellular component: Cellular environment of FIB-sectioned Saccharomyces cerevisiae cell

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Supramolecule #1: Cellular environment of FIB-sectioned Saccharomyces cerevisiae cell

SupramoleculeName: Cellular environment of FIB-sectioned Saccharomyces cerevisiae cell
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: KWY11434(Brr6(I149D))

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 5.8 / Details: Synthetic Complete (SC) with 2% Galactose
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV
Details: Blotted from the backside of the grid. The other side was covered with a teflon sheet..
Details4ul cells at OD2
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 60 / Focused ion beam - Temperature: 119 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 250
Focused ion beam - Details: Procedure as described in https://doi.org/10.7554/eLife.52286. The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. This is not in a list of allowed ...Focused ion beam - Details: Procedure as described in https://doi.org/10.7554/eLife.52286. The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 160.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41
CTF correctionType: NONE

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